The bench scientist's guide to statistical analysis of RNA-Seq data

BMC Research Notes

Table 3 Statistical limitations are revealed by independent analysis of ozone-responsive genes

Functional annotation	Locus ID	Transcript length	Control RPKM	Treatment RPKM	Fold change	DESeq	edgeR	Individual t-test
Light-harvesting complex II CAB protein	Glyma05g25810	1100	7733.20 ± 783.0	4575.86 ± 429.3	0.59	0.063	3.39E-04 *	0.004 *
Ubiquitin	Glyma20g27950	1540	1504.18 ± 149.8	2425.15 ± 206.1	1.61	0.061	0.007 *	0.003 *
Thioredoxin	Glyma17g37280	1134	265.49 ± 11.1	220.79 ± 17.8	0.83	0.14	0.213	0.021 *
L-ascorbate peroxidase	Glyma11g11460	1278	84.73 ± 2.6	107.98 ± 4.4	1.27	0.214	0.272	0.001 *
Polysaccharide catabolism	Glyma06g45700	1831	70.47 ± 8.6	18.91 ± 9.2	0.27	2.34E-29 *	4.48E-19 *	0.002 *
Glutaredoxin	Glyma13g30770	747	11.31 ± 1.4	34.68 ± 6.8	3.07	8.39E-14 *	1.56E-11 *	0.004 *
Protein degradation DER1 like	Glyma04g14250	1088	5.23 ± 0.2	44.52 ± 11.8	8.51	7.06E-49 *	8.30E-38 *	0.005 *
Lipoxygenase	Glyma03g42500	2833	2.90 ± 0.4	5.64 ± 1.3	1.95	1.96E-04 *	2.26E-04 *	0.027 *
Starch synthase catalytic domain	Glyma20g36040	1954	2.84 ± 0.8	0.12 ± 0.1	0.04	1.14E-23 *	1.60E-36 *	0.005 *
WRKY trascription factor	Glyma10g27860	1468	1.69 ± 0.4	70.92 ± 20.80	41.97	9.23E-121 *	2.76E-92 *	0.005 *

Genes known to be regulated by elevated ozone that had a range of transcript abundances were selected from the optimized list of differentially regulated genes. In addition to p-values from DESeq and edgeR, an ANOVA was performed on RPKM values. Asterisks signify p-value below p = 0.05.

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